Global transcriptomic analyses of pluripotent stem cell-derived airway epithelial cells at 1 and 3 days after infection with SARS-CoV-2

We performed transcriptomic profiling of human iPSC-derived airway epithelial cells after infection with SARS-Co-V2. Using a recently described protocol to first generate airway basal cells from iPSCs and sunsequently differentiate those basal cells (iBCs) into a mucociliary epithelium in air-liquid interface culture. In this experiment we generated airway epithelial cultures from two different iPSC lines ("BU3 NGPT" and "1566"). In stage 6 of this protocol (>D45) iBCs are identified and purified by sorting on NGFR+ cells, and purified cells are expanded and differentiated on Transwells in dual-SMAD inhibition media then transitioned to ALI media when >80% confluent. Apical chamber media is removed to initiate ALI to recapitulate a physiologically-relevant environment and stimulate differentiation. After 14 days, iBCs form a pseudostratified airway epithelium that displays morphologic, molecular, and functional similarities to primary human airway epithelial cells and is comprised of the major airway cell types of multi-ciliated, secretory, and basal cellscomposed of the major airway epithelial cell types, that is permissive to SARS-CoV-2 infection. We studied the response of these iPSC-derived airway epithelial cells to SARS-CoV-2 infection using RNA-Sequencing 1 and 3 days post infection (DPI). On day 24 of ALI culture, 6 replicate wells of iPSC-airways from BU3 NGPT were infected with SARS-CoV-2 from the apical surface and 6 replicate wells were mock-infected. Three wells per condition were harvested at each 1 and 3 dpi. 3 replicate wells of 1566 were infected with SARS-CoV-2 in the identical manner and three wells were mock infected. All samples were harvested at 1 dpi.